Epigenetics and DNA Methylation

Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory

This study shows that ROS1-induced DNA demethylation leads to distinct epigenetic changes in chromosome arms and pericentromeres during plant immune memory formation and erasure.

DNA demethylases constrain multigenerational methylome and transcriptome divergence

This study shows that DNA demethylases limit multigenerational methylation and transcriptome divergence by showing that their loss leads to increased methylation gains and transcriptome divergence in Arabidopsis.

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

CellMethMarker provides a database of DNA methylation markers specific to human cell and tissue types, improving deconvolution accuracy in single-cell methylomes.

Predicting Biological Age and Clinical Biomarkers from DNA Methylation Profiles of Cheek Mucosa

This study predicts biological age and clinical biomarkers from cheek mucosa DNA methylation data, showing high accuracy for age and multiple biomarkers compared to blood-derived data.

A new bioinformatic analysis highlights a subpopulation of mitochondria with highly methylated DNA present in oocytes, early embryos and blood.

The paper identifies a subpopulation of highly methylated mtDNA in oocytes, embryos, and blood using single-read methylation analysis, revealing functional heterogeneity among mitochondria.

Male youth BMI is associated with epigenetic ageing of female descendants but not blood or sperm DNA methylation

Epigenetic clocks and nonlinear aging in Odocoileus deer

This study develops epigenetic clocks for mule deer and a multi-species clock for the Odocoileus genus to analyze age-associated DNA methylation patterns and aging dynamics.

Ultra-sensitive Mapping of Cell-free DNA-derived Methylomes Reveals Brain-specific Epigenetic Alterations Implicated in Alzheimer Disease

The paper demonstrates the feasibility of detecting methylation differences in serum-derived cell-free DNA between Alzheimer's disease and non-AD controls using LABS, linking these changes to brain-specific epigenetic alterations in AD.

Protein cofactors diversify PRC2 architecture and function

This study reports cryo-EM structures of PRC2.1 complexes with different cofactors, revealing how they diversify function while maintaining conserved catalytic mechanisms.

Cross-Tissue Concordance of Blood-Trained Protein EpiScores in Donor-Matched GTEx Tissues

This study evaluates how well blood-trained protein EpiScores predict protein levels in non-blood GTEx tissues, finding broad concordance in lung but covariate-sensitive results in other tissues.

A genome-wide catalog of sites where peripheral DNA methylation reflects the brain

The paper identifies brain-peripheral DNA methylation sites (BrESS) that consistently predict brain methylation across tissues, showing they are not linked to disease heritability.

Age-driven miR-29 trades youthful plasticity for epigenetic fidelity

This study identifies miR-29 as a key regulator of age-related epigenetic changes, showing it promotes fidelity but reduces plasticity in methylome maintenance and adaptation.

EpiSignaLR: an open resource for genome-wide episignature analysis from methylation-aware short- and long-read sequencing

The paper develops EpiSignaLR, a resource for genome-wide episignature analysis using methylation-aware sequencing data, identifying DMRs and classifiers for three neurodevelopmental disorders.

Sex Differences in DNA Methylation and Gene Expression Reveal Distinct Molecular Programs in Muscle-Invasive Bladder Cancer

This study identifies sex-associated epigenetic and transcriptional programs in muscle-invasive bladder cancer, showing distinct DNA methylation and gene expression patterns between males and females, with conservation in a mouse model.

RNA m6A mediates de novo DNA methylation and heritable epigenetic silencing in human cells

The paper shows RNA m6A modifications coordinate with de novo DNA methylation to establish heritable epigenetic silencing in human cells.

EG-BINN: Parameter-Efficient Ensembling of Gated Biologically Informed Neural Networks for Epigenetic Age Estimation

EG-BINN improves epigenetic age estimation by combining parameter-efficient ensembling of biologically informed neural networks with sample-specific gating, achieving lower error rates than existing methods.

DNA sequence sets the destination of spontaneous epimutations in plants

The paper shows DNA sequence determines the destination of spontaneous epimutations in plants, using a deep-learning model trained on one methylome to predict methylation set points across species.

FBRSL1 couples ncPRC1.3 to CoREST to repress cell-cycle genes during human neuronal differentiation

This study shows FBRSL1 couples ncPRC1.3 to CoREST for transcriptional repression during neuronal differentiation, contrasting AUTS2's activating role.

A new epigenetic framework for DNA methylation, hydroxymethylation, and gene expression during brain aging.

The paper shows that cell identity and regulatory logic are preserved during brain aging, but cell-type-specific changes occur in DNA modifications and gene expression.

The relevance of GGCC methylation for cyanobacterial gene expression regulation

The paper investigates the impact of GGCC methylation on gene expression in Synechocystis 6803 and finds it affects over 300 genes, with context-specific effects on promoter regions.

DNA methylation alterations in MIR10B, MIR21, MIR100, MIR127 and MIR143 genes associated with advanced carotid artery atherosclerosis: a targeted bisulfite sequencing study of vascular tissues and peripheral blood

LongVerse: verified AI agents for Nanopore and PacBio DNA methylation analysis

LongVerse uses AI agents to generate haplotype-resolved DNA methylation calls from Nanopore and PacBio reads, achieving high agreement with bisulfite sequencing and reducing errors compared to existing methods.

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

EZHIP, a PRC2 inhibitor, arose on the placental mammal X chromosome, evolves under positive selection in primates, and duplicated, including a testis-expressed primate paralog, EZHIP2, whose gorilla copy inhibits H3K27me3.

KDM4 inhibition alters H3K9me3 distribution and developmental responses in SETDB1-deficient embryonic stem cells

This study shows that KDM4 inhibition changes chromatin structure and transcription in embryonic stem cells, with some effects dependent on Setdb1 status.

Subindividual variation in plants: branch-level phenotypic and epigenetic divergence of pollen grains is correlated with the epigenetic divergence of adjacent leaves

The paper examines subindividual epigenetic and phenotypic variation in plants, finding correlations between branch-level epigenetic divergence in leaves and pollen grains from the same branches.

Mitigating genotype-driven bias improves atlas-scale single-cell DNA methylome profiling

The paper mitigates genotype-driven bias in single-cell DNA methylation analysis by masking variant positions, improving clustering and reducing spurious methylation differences in pooled datasets.

PRC2-binding regions are hotspots of DNA methylation entropy in pre-cancer and cancer

The paper identifies PRC2-binding regions as hotspots of DNA methylation variability in pre-cancer and cancer, showing increased entropy and association with aggressive tumor features.

An epigenetic palimpsest: the King penguin's blood methylome reveals conserved hematopoietic ageing

This study identifies conserved ageing-associated genes in King penguins using methylome data and shows their relevance to human epigenetic age prediction.

Exploring the bistable equilibrium of methylated CpG DNA recognition by the MBD2 protein

The paper uses molecular dynamics simulations and experimental assays to show MBD2 binds methylated CpG DNA with a bistable equilibrium, involving two stable conformations with different affinities.

High-performance xenograft read-sorting for DNA methylation analysis

The paper improves a tool for sorting DNA reads in xenograft models, enhancing efficiency for epigenetic analysis.